Merge pull request #11 from tcezard/EVA3322-refactor

EVA-3322 - Use new version of pyutils

.github/workflows/python-package.yml

@@ -16,7 +16,9 @@ jobs:
     strategy:
       matrix:
         python-version: [3.6, 3.8]
-        java-version: [1.8]
+        java-version: [1.11]
+        java-version: [1.11]
+        nextflow-version: [21.10.5]
 
     steps:
     - uses: actions/checkout@v2
@@ -27,8 +29,10 @@ jobs:
         java-version: ${{ matrix.java-version }}
     - name: Set up Nextflow
       run: |
-        sudo bash -c "export JAVA_CMD="$(which java)" && cd /usr/bin && (curl -s https://get.nextflow.io | bash) && chmod 755 nextflow"
-        /usr/bin/nextflow -version
+        mkdir /tmp/nextflow && cd /tmp/nextflow
+        wget -qO- https://github.com/nextflow-io/nextflow/releases/download/v${{ matrix.nextflow-version }}/nextflow-${{ matrix.nextflow-version }}-all | bash
+        echo "/tmp/nextflow" >> $GITHUB_PATH
+        cd -
     - name: Set up BCFtools
       run: |
         sudo apt update

eva_vcf_merge/merge.py

@@ -15,7 +15,7 @@
 import os
 import shutil
 
-from ebi_eva_common_pyutils.nextflow import NextFlowPipeline, NextFlowProcess
+from ebi_eva_internal_pyutils.nextflow import NextFlowPipeline, NextFlowProcess
 
 from eva_vcf_merge.detect import MergeType
 from eva_vcf_merge.multistage import get_multistage_merge_pipeline

eva_vcf_merge/multistage.py

@@ -15,7 +15,7 @@
 import math
 import os
 
-from ebi_eva_common_pyutils.nextflow import NextFlowPipeline, NextFlowProcess
+from ebi_eva_internal_pyutils.nextflow import NextFlowPipeline, NextFlowProcess
 
 
 def get_multistage_merge_pipeline(

requirements.txt

@@ -1,3 +1,3 @@
-ebi_eva_common_pyutils>=0.3.22
+ebi-eva-common-pyutils[eva-internal]==0.6.0
 pysam~=0.16
 pytest~=6.2